Contacts of the strand formed by residues 84 - 99 (chain E) in PDB entry 1KN0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 84 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E PHE* 3.9 2.0 - - - -
72E ILE* 4.3 12.3 - - + -
75E ALA* 3.7 26.0 - - + -
76E ASN* 3.3 23.1 + - - +
79E PHE* 3.7 19.7 - + + -
80E GLY 3.4 16.6 - - - -
81E TYR 4.2 2.4 + - - +
83E GLY* 1.3 78.6 - - - +
85E ALA* 1.3 68.7 + - - +
86E HIS* 4.5 2.7 - - + -
113E VAL* 3.7 22.0 - - + -
114E GLN 3.3 7.4 - - - +
115E LEU* 4.0 9.0 - - + +
151E LEU* 3.8 38.1 - - + -
155E LEU* 4.0 13.9 - - + -
119F SER* 3.8 13.2 + - - -
121F HIS* 3.2 40.0 + + - -
157F SER* 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E PHE* 3.7 16.4 - - + -
84E TRP* 1.3 80.3 - - - +
86E HIS* 1.3 59.9 + - - +
113E VAL* 3.1 7.8 - - - +
114E GLN 2.7 32.4 + - - +
120F TYR* 2.8 51.6 - - + +
121F HIS* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E TRP* 4.5 2.0 - + + -
85E ALA* 1.3 76.1 - - - +
87E SER* 1.3 61.4 + - - +
88E ILE* 5.8 0.4 - - + +
111E VAL* 3.9 20.7 - - + +
112E ARG 3.1 11.2 - - - +
113E VAL* 4.2 3.4 - - + -
147E VAL* 5.2 5.1 - - + +
151E LEU* 3.4 42.2 - - + +
120F TYR* 3.1 22.1 + - - -
121F HIS* 3.0 46.5 - + - +
122F GLU 3.2 32.1 + - - -
123F ASP* 4.5 9.0 - - - -
157F SER* 3.5 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E HIS* 1.3 77.1 - - - +
88E ILE* 1.3 66.0 + - - +
89E THR* 3.6 3.3 + - - -
111E VAL* 3.4 6.3 - - - +
112E ARG* 3.0 43.4 + - - +
112F ARG* 5.0 7.4 - - - -
120F TYR* 3.8 18.6 + - - -
122F GLU* 3.3 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E HIS* 5.8 0.4 - - - +
87E SER* 1.3 72.8 - - - +
89E THR* 1.3 65.9 + - - +
90E GLN* 3.7 23.6 - - - +
91E GLN* 4.3 5.8 - - + +
109E ALA* 4.8 4.7 - - + -
110E PHE 3.6 10.8 - - - +
111E VAL* 4.6 6.5 - - + +
147E VAL* 3.6 31.9 - - + -
89F THR* 5.7 2.1 - - - +
110F PHE* 3.7 32.5 - - + -
122F GLU* 2.5 37.8 + - + +
123F ASP* 3.8 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ILE 5.7 2.5 - - - +
87E SER* 3.6 4.7 + - - -
88E ILE* 1.3 74.3 - - - +
90E GLN* 1.3 67.3 + - + +
110E PHE* 2.8 15.3 + - + -
112E ARG* 4.0 17.7 - - - +
122E GLU* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ILE* 3.3 7.5 - - - +
89E THR* 1.3 89.8 - - + +
91E GLN* 1.3 71.9 + - - +
92E ASN* 4.6 8.7 - - + +
109E ALA* 3.3 1.0 - - - -
110E PHE* 2.6 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ILE* 4.3 2.4 - - + +
90E GLN* 1.3 80.3 - - - +
92E ASN* 1.3 64.2 + - - +
93E VAL 4.3 0.2 + - - -
107E VAL* 3.7 13.8 - - + +
108E CYS 3.3 12.6 - - - +
109E ALA* 4.0 9.7 - - + +
143E ARG* 2.8 74.8 + - - +
147E VAL* 3.9 8.6 - - - +
110F PHE* 3.0 43.0 - - + -
124F VAL* 3.8 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ARG* 4.5 7.3 - - - +
90E GLN* 4.3 13.2 - - + +
91E GLN* 1.3 75.0 - - - +
93E VAL* 1.3 71.0 + - - +
94E ASP* 3.2 25.6 + - - +
107E VAL* 4.3 2.2 - - - -
108E CYS* 2.9 44.4 + - - -
110E PHE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ASN* 1.3 79.5 + - - +
94E ASP* 1.3 64.8 + - - +
95E PHE* 3.9 8.5 - - - +
96E VAL* 3.8 29.2 - - + -
107E VAL* 3.9 24.0 - - + -
139E LEU* 4.3 7.2 - - + -
143E ARG* 3.5 39.7 - - - +
94F ASP* 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL* 5.0 1.2 - - - +
139D LEU* 3.1 24.8 - - + +
143D ARG* 2.5 30.1 + - - -
92E ASN* 3.2 18.9 + - - +
93E VAL* 1.3 73.4 - - - +
95E PHE* 1.3 64.3 + - + +
106E GLY 2.7 15.4 + - - +
108E CYS* 4.7 0.2 - - - -
126E TYR* 2.6 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LYS* 3.3 48.2 - - + +
136D ALA* 3.3 35.9 - - + -
139D LEU* 3.9 10.1 - - + -
93E VAL* 3.4 3.1 - - - +
94E ASP* 1.3 90.5 - - + +
96E VAL* 1.3 73.6 + - - +
97E ASP* 3.6 15.0 - - - +
104E TYR* 3.1 32.1 - - + -
105E VAL* 3.4 3.9 - - - +
106E GLY* 3.2 41.6 + - - +
130E GLU* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 3.8 11.4 - - + -
95E PHE* 1.3 83.6 - - - +
97E ASP* 1.3 62.8 + - - +
98E LEU* 4.2 0.7 + - - +
103E PHE* 4.4 10.4 - - + -
104E TYR 3.7 3.8 - - - -
105E VAL* 3.8 15.0 - - + -
135E LYS* 4.1 27.8 - - + -
139E LEU* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LYS* 2.7 39.8 + - - -
95E PHE* 3.6 8.2 - - - +
96E VAL* 1.3 80.7 + - - +
98E LEU* 1.3 60.1 + - - +
99E ASN* 4.1 10.5 - - - +
102E LYS 3.8 0.3 - - - +
103E PHE* 3.4 9.1 - - - -
104E TYR* 2.9 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E VAL 4.2 0.8 + - - +
97E ASP* 1.3 73.9 - - - +
99E ASN* 1.3 64.5 + - - +
100E ASN 4.0 1.9 + - - +
101E GLY* 3.7 17.0 - - - +
102E LYS 3.0 33.4 - - - +
103E PHE* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ASP* 4.1 9.4 - - - +
98E LEU* 1.3 76.7 - - - +
100E ASN* 1.3 88.2 + - - +
101E GLY 3.6 0.2 - - - -
102E LYS* 3.0 22.3 + - - +
104E TYR* 3.7 38.0 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il